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OPENSEQ.org
1ixr_C_B
Genes: A B A+B
Length: 312 191 500
Sequences: 2672 2889 1700
Seq/Len: 8.56 15.13 3.4
MirrorTree (Pazo et al. 2001) 0.75
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.08 0.09 3.02
2 0.08 0.09 3.17
5 0.08 0.09 3.30
10 0.08 0.09 3.35
20 0.08 0.09 3.38
100 0.08 0.09 3.48
∞ 0.09 0.09 4.05
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
76_K 162_Q 3.20 1.00 1.00
121_I 155_A 1.02 0.70 0.55
130_R 148_E 0.97 0.65 0.49
191_E 142_E 0.96 0.64 0.48
226_I 128_K 0.96 0.64 0.47
133_R 84_V 0.95 0.63 0.46
172_E 17_F 0.94 0.61 0.45
135_E 184_K 0.93 0.60 0.43
25_R 188_K 0.91 0.57 0.41
167_Y 3_R 0.90 0.57 0.40
65_N 128_K 0.90 0.56 0.40
281_L 185_E 0.90 0.56 0.40
126_G 126_E 0.90 0.56 0.39
123_I 148_E 0.89 0.56 0.39
295_L 106_A 0.89 0.56 0.39
167_Y 148_E 0.89 0.55 0.39
169_T 147_E 0.87 0.53 0.37
62_L 41_G 0.86 0.52 0.36
85_A 183_I 0.85 0.50 0.34
27_Y 124_A 0.84 0.49 0.33
44_F 49_H 0.84 0.49 0.33
307_L 78_S 0.84 0.49 0.33
124_G 83_K 0.84 0.48 0.33
212_R 27_F 0.82 0.47 0.31
208_K 125_L 0.82 0.46 0.31
260_F 180_Q 0.82 0.46 0.30
109_H 186_A 0.80 0.44 0.28
119_M 80_V 0.80 0.43 0.28
171_E 47_H 0.80 0.43 0.28
76_K 109_L 0.80 0.43 0.28
142_I 111_S 0.79 0.43 0.28
162_V 106_A 0.79 0.42 0.27
23_K 51_L 0.78 0.41 0.26
134_L 119_L 0.77 0.40 0.25
114_M 105_D 0.77 0.40 0.25
257_I 17_F 0.77 0.40 0.25
254_E 37_A 0.77 0.40 0.25
58_I 60_Y 0.76 0.38 0.23
24_L 100_A 0.75 0.38 0.23
26_V 162_Q 0.75 0.38 0.23
177_V 70_L 0.75 0.37 0.23
200_S 95_R 0.75 0.37 0.23
55_A 20_L 0.74 0.37 0.23
269_T 76_S 0.74 0.37 0.22
44_F 148_E 0.74 0.36 0.22
183_L 92_L 0.74 0.36 0.22
74_I 57_L 0.73 0.35 0.21
60_H 47_H 0.73 0.35 0.21
35_K 69_A 0.73 0.35 0.21
215_R 127_L 0.73 0.35 0.21
34_R 122_R 0.73 0.35 0.21
171_E 37_A 0.73 0.35 0.21
117_F 142_E 0.72 0.34 0.21
14_Y 68_L 0.72 0.34 0.20
180_D 125_L 0.72 0.34 0.20
258_L 111_S 0.71 0.33 0.19
187_R 139_E 0.71 0.33 0.19
162_V 105_D 0.71 0.33 0.19
89_E 188_K 0.71 0.33 0.19
76_K 158_F 0.71 0.32 0.19
71_G 25_G 0.71 0.32 0.19
130_R 2_I 0.70 0.32 0.19
250_R 183_I 0.70 0.32 0.19
170_P 40_E 0.70 0.32 0.18
167_Y 67_N 0.70 0.32 0.18
68_V 111_S 0.70 0.32 0.18
295_L 6_R 0.70 0.31 0.18
34_R 126_E 0.69 0.31 0.18
260_F 68_L 0.69 0.31 0.18
240_L 87_A 0.69 0.31 0.18
78_G 187_L 0.69 0.31 0.17
119_M 57_L 0.69 0.31 0.17
135_E 80_V 0.69 0.30 0.17
136_L 131_V 0.69 0.30 0.17
24_L 73_L 0.69 0.30 0.17
282_E 55_E 0.68 0.30 0.17
189_T 178_R 0.68 0.30 0.17
283_E 162_Q 0.68 0.29 0.17
37_P 80_V 0.68 0.29 0.16
29_E 42_K 0.68 0.29 0.16
74_I 73_L 0.68 0.29 0.16
294_L 105_D 0.67 0.29 0.16
121_I 152_A 0.67 0.29 0.16
256_L 183_I 0.67 0.29 0.16
304_A 33_P 0.67 0.28 0.16
13_E 155_A 0.67 0.28 0.16
112_P 79_G 0.67 0.28 0.16
152_T 190_L 0.67 0.28 0.16
283_E 92_L 0.67 0.28 0.16
281_L 37_A 0.67 0.28 0.15
162_V 49_H 0.67 0.28 0.15
143_G 82_P 0.66 0.28 0.15
140_T 153_L 0.66 0.28 0.15
295_L 135_L 0.66 0.28 0.15
78_G 190_L 0.66 0.27 0.15
290_I 49_H 0.66 0.27 0.15
55_A 3_R 0.66 0.27 0.15
119_M 107_R 0.66 0.27 0.15
74_I 166_V 0.66 0.27 0.15
60_H 115_V 0.66 0.27 0.15
74_I 76_S 0.66 0.27 0.15
238_L 77_V 0.66 0.27 0.15
191_E 138_G 0.66 0.27 0.15
12_D 66_E 0.66 0.27 0.15
20_L 73_L 0.65 0.27 0.14
184_L 121_E 0.65 0.27 0.14
119_M 105_D 0.65 0.26 0.14
75_E 109_L 0.65 0.26 0.14
138_R 167_V 0.65 0.26 0.14
303_V 111_S 0.65 0.26 0.14
190_E 170_L 0.65 0.26 0.14
284_V 48_T 0.65 0.26 0.14
142_I 108_L 0.64 0.26 0.14
281_L 138_G 0.64 0.26 0.14
279_G 28_L 0.64 0.26 0.14
212_R 159_K 0.64 0.25 0.14
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
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